data_D7K # _chem_comp.id D7K _chem_comp.name "3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-2-{(S)-hydroxy[(R)-hydroxy(methoxy)phosphoryl]phenylmethyl}-5-(2-{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-3-ium" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C20 H28 N4 O11 P3 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 1 _chem_comp.pdbx_initial_date 2008-05-22 _chem_comp.pdbx_modified_date 2011-06-04 _chem_comp.pdbx_ambiguous_flag N _chem_comp.pdbx_release_status REL _chem_comp.pdbx_replaced_by ? _chem_comp.pdbx_replaces ? _chem_comp.formula_weight 625.443 _chem_comp.one_letter_code ? _chem_comp.three_letter_code D7K _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 3D7K _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.alt_atom_id _chem_comp_atom.type_symbol _chem_comp_atom.charge _chem_comp_atom.pdbx_align _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_leaving_atom_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.model_Cartn_x _chem_comp_atom.model_Cartn_y _chem_comp_atom.model_Cartn_z _chem_comp_atom.pdbx_model_Cartn_x_ideal _chem_comp_atom.pdbx_model_Cartn_y_ideal _chem_comp_atom.pdbx_model_Cartn_z_ideal _chem_comp_atom.pdbx_component_atom_id _chem_comp_atom.pdbx_component_comp_id _chem_comp_atom.pdbx_ordinal D7K PA PA P 0 1 N N R -42.169 27.537 2.473 5.432 -0.266 0.186 PA D7K 1 D7K O1A O1A O 0 1 N N N -42.418 28.222 0.998 5.366 0.036 1.633 O1A D7K 2 D7K O2A O2A O 0 1 N N N -43.519 27.421 3.035 5.460 -1.862 -0.028 O2A D7K 3 D7K O1B O1B O 0 1 N N N -39.852 30.386 4.051 9.030 -0.953 -0.341 O1B D7K 4 D7K PB PB P 0 1 N N N -39.781 28.884 3.428 8.307 0.437 0.030 PB D7K 5 D7K O2B O2B O 0 1 N N N -39.277 28.852 1.848 8.372 0.653 1.492 O2B D7K 6 D7K O3B O3B O 0 1 N N N -38.934 27.971 4.129 9.053 1.648 -0.725 O3B D7K 7 D7K O3A O3A O 0 1 N N N -41.364 28.507 3.489 6.767 0.382 -0.437 O3A D7K 8 D7K O01 O01 O 0 1 N N N -41.524 26.064 2.226 4.141 0.352 -0.550 O01 D7K 9 D7K C01 C01 C 0 1 N N N -41.359 25.230 3.353 2.801 0.055 -0.152 C01 D7K 10 D7K C05 C05 C 0 1 N N N -40.155 24.298 3.093 1.821 0.804 -1.058 C05 D7K 11 D7K C04 C04 C 0 1 Y N N -40.305 23.026 3.932 0.408 0.491 -0.638 C04 D7K 12 D7K C03 C03 C 0 1 Y N N -40.949 21.766 3.604 -0.315 1.172 0.256 C03 D7K 13 D7K CM4 CM4 C 0 1 N N N -41.612 21.392 2.263 0.214 2.383 0.981 CM4 D7K 14 D7K S1 S1 S 0 1 Y N N -39.701 23.032 5.556 -0.584 -0.833 -1.243 S1 D7K 15 D7K C02 C02 C 0 1 Y N N -40.089 21.477 6.068 -1.870 -0.344 -0.229 C02 D7K 16 D7K N3 N3 N 1 1 Y N N -40.845 20.798 4.900 -1.529 0.697 0.452 N3 D7K 17 D7K C7, C7, C 0 1 N N N -41.296 19.411 4.978 -2.452 1.327 1.399 C7, D7K 18 D7K C5, C5, C 0 1 Y N N -42.806 19.325 4.971 -3.315 2.326 0.672 C5, D7K 19 D7K C6, C6, C 0 1 Y N N -43.444 18.719 3.921 -2.770 3.182 -0.264 C6, D7K 20 D7K C4, C4, C 0 1 Y N N -43.515 19.778 6.093 -4.686 2.405 0.924 C4, D7K 21 D7K N4, N4, N 0 1 N N N -42.878 20.391 7.226 -5.281 1.564 1.850 N4, D7K 22 D7K N3, N3, N 0 1 Y N N -44.818 19.728 6.086 -5.412 3.300 0.260 N3, D7K 23 D7K C2, C2, C 0 1 Y N N -45.501 19.147 5.046 -4.849 4.102 -0.621 C2, D7K 24 D7K N1, N1, N 0 1 Y N N -44.787 18.624 4.009 -3.559 4.048 -0.885 N1, D7K 25 D7K CM2 CM2 C 0 1 N N N -47.028 19.049 5.100 -5.705 5.103 -1.353 CM2 D7K 26 D7K O12 O12 O 0 1 N N N -38.323 18.587 6.046 -2.048 -3.115 -1.410 O12 D7K 27 D7K P8 P8 P 0 1 N N R -38.035 19.879 7.024 -3.306 -2.336 -1.412 P8 D7K 28 D7K O11 O11 O 0 1 N N N -37.221 20.843 6.246 -4.543 -3.312 -1.083 O11 D7K 29 D7K O9 O9 O 0 1 N N N -37.373 19.386 8.476 -3.521 -1.667 -2.860 O9 D7K 30 D7K C10 C10 C 0 1 N N N -36.278 20.066 9.043 -3.531 -2.422 -4.073 C10 D7K 31 D7K C7 C7 C 0 1 N N S -39.593 20.830 7.391 -3.211 -1.027 -0.146 C7 D7K 32 D7K O7 O7 O 0 1 N N N -40.602 19.944 7.790 -4.248 -0.070 -0.372 O7 D7K 33 D7K C2 C2 C 0 1 Y N N -39.310 21.947 8.436 -3.380 -1.638 1.221 C2 D7K 34 D7K C3 C3 C 0 1 Y N N -40.159 22.124 9.550 -4.619 -1.625 1.836 C3 D7K 35 D7K C4 C4 C 0 1 Y N N -39.917 23.168 10.474 -4.774 -2.185 3.090 C4 D7K 36 D7K C5 C5 C 0 1 Y N N -38.823 24.067 10.258 -3.691 -2.758 3.730 C5 D7K 37 D7K C6 C6 C 0 1 Y N N -37.973 23.882 9.162 -2.452 -2.771 3.115 C6 D7K 38 D7K C1 C1 C 0 1 Y N N -38.198 22.834 8.263 -2.298 -2.216 1.859 C1 D7K 39 D7K HO2A HO2A H 0 0 N N N -43.467 27.396 3.983 5.503 -2.133 -0.955 HO2A D7K 40 D7K HO1B HO1B H 0 0 N N N -39.866 30.336 5.000 9.026 -1.159 -1.285 HO1B D7K 41 D7K HO3B HO3B H 0 0 N N N -38.746 27.223 3.574 9.987 1.741 -0.491 HO3B D7K 42 D7K H01 H01 H 0 1 N N N -41.172 25.842 4.247 2.626 -1.018 -0.236 H01 D7K 43 D7K H01A H01A H 0 0 N N N -42.269 24.635 3.521 2.651 0.368 0.882 H01A D7K 44 D7K H05 H05 H 0 1 N N N -40.121 24.032 2.026 1.996 1.876 -0.974 H05 D7K 45 D7K H05A H05A H 0 0 N N N -39.224 24.814 3.372 1.971 0.491 -2.091 H05A D7K 46 D7K HM4 HM4 H 0 1 N N N -42.699 21.303 2.403 -0.016 3.279 0.405 HM4 D7K 47 D7K HM4A HM4A H 0 0 N N N -41.401 22.174 1.519 -0.254 2.451 1.963 HM4A D7K 48 D7K HM4B HM4B H 0 0 N N N -41.208 20.432 1.910 1.294 2.293 1.098 HM4B D7K 49 D7K H7, H7, H 0 1 N N N -40.904 18.860 4.111 -3.084 0.564 1.853 H7, D7K 50 D7K H7,A H7,A H 0 0 N N N -40.926 18.976 5.918 -1.883 1.837 2.177 H7,A D7K 51 D7K H6, H6, H 0 1 N N N -42.901 18.338 3.069 -1.714 3.147 -0.488 H6, D7K 52 D7K HN4, HN4, H 0 0 N N N -41.908 20.533 7.027 -4.734 0.972 2.389 HN4, D7K 53 D7K HN4A HN4A H 0 0 N N N -43.312 21.272 7.416 -6.245 1.567 1.960 HN4A D7K 54 D7K HM2 HM2 H 0 1 N N N -47.358 19.025 6.149 -5.737 6.035 -0.789 HM2 D7K 55 D7K HM2A HM2A H 0 0 N N N -47.469 19.922 4.597 -5.283 5.289 -2.340 HM2A D7K 56 D7K HM2B HM2B H 0 0 N N N -47.354 18.129 4.593 -6.716 4.708 -1.458 HM2B D7K 57 D7K HO11 HO11 H 0 0 N N N -37.047 21.612 6.776 -5.401 -2.868 -1.067 HO11 D7K 58 D7K H10 H10 H 0 1 N N N -35.516 20.243 8.270 -4.333 -3.159 -4.035 H10 D7K 59 D7K H10A H10A H 0 0 N N N -36.617 21.030 9.452 -3.692 -1.752 -4.918 H10A D7K 60 D7K H10B H10B H 0 0 N N N -35.846 19.456 9.850 -2.574 -2.932 -4.191 H10B D7K 61 D7K HO7 HO7 H 0 1 N N N -40.501 19.743 8.713 -5.133 -0.456 -0.432 HO7 D7K 62 D7K H3 H3 H 0 1 N N N -40.997 21.459 9.698 -5.465 -1.177 1.336 H3 D7K 63 D7K H4 H4 H 0 1 N N N -40.554 23.286 11.338 -5.741 -2.175 3.570 H4 D7K 64 D7K H5 H5 H 0 1 N N N -38.654 24.887 10.940 -3.812 -3.195 4.710 H5 D7K 65 D7K H6 H6 H 0 1 N N N -37.139 24.551 9.009 -1.606 -3.218 3.615 H6 D7K 66 D7K H1 H1 H 0 1 N N N -37.526 22.692 7.429 -1.332 -2.230 1.377 H1 D7K 67 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal D7K PA O2A SING N N 1 D7K PA O3A SING N N 2 D7K O1A PA DOUB N N 3 D7K O2A HO2A SING N N 4 D7K O1B HO1B SING N N 5 D7K PB O1B SING N N 6 D7K PB O3A SING N N 7 D7K PB O3B SING N N 8 D7K O2B PB DOUB N N 9 D7K O3B HO3B SING N N 10 D7K O01 PA SING N N 11 D7K O01 C01 SING N N 12 D7K C01 H01 SING N N 13 D7K C01 H01A SING N N 14 D7K C05 C01 SING N N 15 D7K C05 C04 SING N N 16 D7K C05 H05 SING N N 17 D7K C05 H05A SING N N 18 D7K C04 S1 SING Y N 19 D7K C03 C04 DOUB Y N 20 D7K C03 N3 SING Y N 21 D7K CM4 C03 SING N N 22 D7K CM4 HM4 SING N N 23 D7K CM4 HM4A SING N N 24 D7K CM4 HM4B SING N N 25 D7K S1 C02 SING Y N 26 D7K C02 C7 SING N N 27 D7K N3 C02 DOUB Y N 28 D7K N3 C7, SING N N 29 D7K C7, H7, SING N N 30 D7K C7, H7,A SING N N 31 D7K C5, C7, SING N N 32 D7K C5, C4, SING Y N 33 D7K C6, C5, DOUB Y N 34 D7K C6, N1, SING Y N 35 D7K C6, H6, SING N N 36 D7K C4, N4, SING N N 37 D7K N4, HN4, SING N N 38 D7K N4, HN4A SING N N 39 D7K N3, C4, DOUB Y N 40 D7K C2, N3, SING Y N 41 D7K C2, CM2 SING N N 42 D7K N1, C2, DOUB Y N 43 D7K CM2 HM2 SING N N 44 D7K CM2 HM2A SING N N 45 D7K CM2 HM2B SING N N 46 D7K O12 P8 DOUB N N 47 D7K P8 C7 SING N N 48 D7K P8 O9 SING N N 49 D7K O11 P8 SING N N 50 D7K O11 HO11 SING N N 51 D7K O9 C10 SING N N 52 D7K C10 H10 SING N N 53 D7K C10 H10A SING N N 54 D7K C10 H10B SING N N 55 D7K C7 O7 SING N N 56 D7K C7 C2 SING N N 57 D7K O7 HO7 SING N N 58 D7K C2 C3 SING Y N 59 D7K C3 C4 DOUB Y N 60 D7K C3 H3 SING N N 61 D7K C4 H4 SING N N 62 D7K C5 C4 SING Y N 63 D7K C5 H5 SING N N 64 D7K C6 C5 DOUB Y N 65 D7K C6 H6 SING N N 66 D7K C1 C2 DOUB Y N 67 D7K C1 C6 SING Y N 68 D7K C1 H1 SING N N 69 # loop_ _pdbx_chem_comp_descriptor.comp_id _pdbx_chem_comp_descriptor.type _pdbx_chem_comp_descriptor.program _pdbx_chem_comp_descriptor.program_version _pdbx_chem_comp_descriptor.descriptor D7K SMILES ACDLabs 10.04 "O=P(O)(OP(=O)(O)O)OCCc1sc([n+](c1C)Cc2cnc(nc2N)C)C(O)(c3ccccc3)P(=O)(OC)O" D7K SMILES_CANONICAL CACTVS 3.341 "CO[P@@](O)(=O)[C@@](O)(c1ccccc1)c2sc(CCO[P@](O)(=O)O[P](O)(O)=O)c(C)[n+]2Cc3cnc(C)nc3N" D7K SMILES CACTVS 3.341 "CO[P](O)(=O)[C](O)(c1ccccc1)c2sc(CCO[P](O)(=O)O[P](O)(O)=O)c(C)[n+]2Cc3cnc(C)nc3N" D7K SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C@@](c3ccccc3)(O)[P@@](=O)(O)OC)CCO[P@@](=O)(O)OP(=O)(O)O" D7K SMILES "OpenEye OEToolkits" 1.5.0 "Cc1c(sc([n+]1Cc2cnc(nc2N)C)C(c3ccccc3)(O)P(=O)(O)OC)CCOP(=O)(O)OP(=O)(O)O" D7K InChI InChI 1.03 "InChI=1S/C20H27N4O11P3S/c1-13-17(9-10-34-38(31,32)35-37(28,29)30)39-19(24(13)12-15-11-22-14(2)23-18(15)21)20(25,36(26,27)33-3)16-7-5-4-6-8-16/h4-8,11,25H,9-10,12H2,1-3H3,(H5-,21,22,23,26,27,28,29,30,31,32)/p+1/t20-/m0/s1" D7K InChIKey InChI 1.03 NEEQBMRCDKRNBV-FQEVSTJZSA-O # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version _pdbx_chem_comp_identifier.identifier D7K "SYSTEMATIC NAME" ACDLabs 10.04 "3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-2-{(S)-hydroxy[(R)-hydroxy(methoxy)phosphoryl]phenylmethyl}-5-(2-{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-3-ium" D7K "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(S)-[3-[(4-amino-2-methyl-pyrimidin-5-yl)methyl]-5-[2-(hydroxy-phosphonooxy-phosphoryl)oxyethyl]-4-methyl-1,3-thiazol-3-ium-2-yl]-hydroxy-phenyl-methyl]-methoxy-phosphinic acid" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site D7K "Create component" 2008-05-22 RCSB D7K "Modify descriptor" 2011-06-04 RCSB #